About: The effect of variant interference on de novo assembly for viral deep sequencing

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	The effect of variant interference on de novo assembly for viral deep sequencing
Creator	Fei, Terry Marine, Rachel Ng, Fan Castro, Christina Ramos, Edward
source	BioRxiv; MedRxiv
abstract	Viruses have high mutation rates and generally exist as a mixture of variants in biological samples. Next-generation sequencing (NGS) approach has surpassed Sanger for generating long viral sequences, yet how variants affect NGS de novo assembly remains largely unexplored. Our results from >15,000 simulated experiments showed that presence of variants can turn an assembly of one genome into tens to thousands of contigs. This “variant interference” (VI) is highly consistent and reproducible by ten most used de novo assemblers, and occurs independent of genome length, read length, and GC content. The main driver of VI is pairwise identities between viral variants. These findings were further supported by in silico simulations, where selective removal of minor variant reads from clinical datasets allow the “rescue” of full viral genomes from fragmented contigs. These results call for careful interpretation of contigs and contig numbers from de novo assembly in viral deep sequencing.
has issue date	2019-10-22(xsd:dateTime)
bibo:doi	10.1101/815480
has license	medrxiv
sha1sum (hex)	1ab72d9b1f4c39bdce18979376014b725ddb7d14
schema:url	https://doi.org/10.1101/815480
resource representing a document's title	The effect of variant interference on de novo assembly for viral deep sequencing
schema:publication	bioRxiv
resource representing a document's body	covid:1ab72d9b1f4c39bdce18979376014b725ddb7d14#body_text
is schema:about of	named entity 'viral' named entity 'pairwise' named entity 'Next' named entity 'rescue' named entity 'de novo assembly' »more»

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